Stimulated and coherent anti-stokes raman spectroscopic methods for the detection of molecules

Abstract

Spectroscopic analysis systems and methods for analyzing samples are disclosed which exploit inelastically scattering radiation to amplify optical signals from an irradiated sample. Samples are irradiated in a chamber having a resonant cavity containing a plurality of affixed reflectors, where selective Stokes scattered radiation is transmitted to a detector for determination of sample identity. Coupling the spectroscopic analysis system and method with a nucleic acid sequencing system is also disclosed for determining nucleic acid sequences.

1. A method for determining the identity of a plurality of molecules of interest in a sample comprising:
 determining a Stokes Raman shift for at least two known molecules of interest; 
 exciting the sample in a resonance chamber, which chamber comprises a reflector and a partial reflector, with at least two light sources, wherein a predetermined distance between reflectors is a function of wave length corresponding to prominent peaks in the Raman spectra for the two known molecules of interest, thereby selectively inelastically scattering radiation from the sample; 
 resonating the inelastically scattered radiation between the reflector and partial reflector to amplify the intensity of the inelastically scattered radiation; 
 transmitting the amplified inelastically scattered radiation from the chamber; 
 detecting the transmitted amplified inelastically scattered radiation; and 
 determining whether the detected transmitted amplified inelastically scattered radiation corresponds to one of the two known molecules of interest. 
 
     
     
       2. The method of  claim 1 , wherein the at least two light sources irradiate in two directions, comprising a seed radiation in a first direction and a transverse radiation in a second direction, the first direction being perpendicular to the second direction. 
     
     
       3. The method of  claim 2 , wherein the seed radiation and transverse radiation are different frequencies. 
     
     
       4. The method of  claim 2 , wherein detecting the separate transmitted amplified inelastically scattered radiation includes detecting a gain over the intensity of the seed radiation. 
     
     
       5. The method of  claim 1 , wherein the reflectors are opposite and parallel to one another within the resonance chamber and centered along a common optical axis. 
     
     
       6. The method of  claim 1 , wherein the predetermined distance provides a nondestructive relationship between the phases of incident and reflected radiation. 
     
     
       7. The method of  claim 1 , wherein the reflectors are multi-layer dielectric mirrors. 
     
     
       8. The method of  claim 7 , wherein the multi-layer dielectric minors contain a layer having a thickness that is based on wavelengths of the separate inelastically scattered radiation for the at least two molecules of interest. 
     
     
       9. The method of  claim 1 , wherein the reflectors include a partial reflector having sufficient reflectivity to achieve resonance and a sufficient transmittance for the separate amplified inelastically scattered radiation. 
     
     
       10. The method of  claim 1 , transmitting the separate scattered radiation comprises transmitting the separate amplified inelastically scattered radiation through an outlet window in the partial reflector. 
     
     
       11. The method of  claim 1 , wherein the resonance chamber includes at least one window to transmit radiation into the chamber and to transmit the separate amplified inelastically scattered radiation out of the chamber.